Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles)

Christopher R. Kinsinger, James Apffel, Mark Baker, Xiaopeng Bian, Christoph H. Borchers, Ralph Bradshaw, Mi Youn Brusniak, Daniel Wan-Yui Chan, Eric W. Deutsch, Bruno Domon, Jeff Gorman, Rudolf Grimm, William Hancock, Henning Hermjakob, David Horn, Christie Hunter, Patrik Kolar, Hans Joachim Kraus, Hanno Langen, Rune LindingRobert L. Moritz, Gilbert S. Omenn, Ron Orlando, Akhilesh Pandey, Peipei Ping, Amir Rahbar, Robert Rivers, Sean L. Seymour, Richard J. Simpson, Douglas Slotta, Richard D. Smith, Stephen E. Stein, David L. Tabb, Danilo Tagle, John R. Yates, Henry Rodriguez

Research output: Contribution to journalArticle

Abstract

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (1) an evolving list of comprehensive quality metrics and (2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data.By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.

Original languageEnglish (US)
Pages (from-to)1412-1419
Number of pages8
JournalJournal of Proteome Research
Volume11
Issue number2
DOIs
StatePublished - Feb 3 2012

Fingerprint

Proteomics
Mass spectrometry
Mass Spectrometry
Education
Research
Peer Review
National Cancer Institute (U.S.)
Data Accuracy
Information Dissemination
Proteome
Software

Keywords

  • Amsterdam Principles
  • bioinformatics
  • data quality
  • metrics
  • open access
  • selected reaction monitoring
  • standards

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R., ... Rodriguez, H. (2012). Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles). Journal of Proteome Research, 11(2), 1412-1419. https://doi.org/10.1021/pr201071t

Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles). / Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi Youn; Chan, Daniel Wan-Yui; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R.; Rodriguez, Henry.

In: Journal of Proteome Research, Vol. 11, No. 2, 03.02.2012, p. 1412-1419.

Research output: Contribution to journalArticle

Kinsinger, CR, Apffel, J, Baker, M, Bian, X, Borchers, CH, Bradshaw, R, Brusniak, MY, Chan, DW-Y, Deutsch, EW, Domon, B, Gorman, J, Grimm, R, Hancock, W, Hermjakob, H, Horn, D, Hunter, C, Kolar, P, Kraus, HJ, Langen, H, Linding, R, Moritz, RL, Omenn, GS, Orlando, R, Pandey, A, Ping, P, Rahbar, A, Rivers, R, Seymour, SL, Simpson, RJ, Slotta, D, Smith, RD, Stein, SE, Tabb, DL, Tagle, D, Yates, JR & Rodriguez, H 2012, 'Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles)', Journal of Proteome Research, vol. 11, no. 2, pp. 1412-1419. https://doi.org/10.1021/pr201071t
Kinsinger, Christopher R. ; Apffel, James ; Baker, Mark ; Bian, Xiaopeng ; Borchers, Christoph H. ; Bradshaw, Ralph ; Brusniak, Mi Youn ; Chan, Daniel Wan-Yui ; Deutsch, Eric W. ; Domon, Bruno ; Gorman, Jeff ; Grimm, Rudolf ; Hancock, William ; Hermjakob, Henning ; Horn, David ; Hunter, Christie ; Kolar, Patrik ; Kraus, Hans Joachim ; Langen, Hanno ; Linding, Rune ; Moritz, Robert L. ; Omenn, Gilbert S. ; Orlando, Ron ; Pandey, Akhilesh ; Ping, Peipei ; Rahbar, Amir ; Rivers, Robert ; Seymour, Sean L. ; Simpson, Richard J. ; Slotta, Douglas ; Smith, Richard D. ; Stein, Stephen E. ; Tabb, David L. ; Tagle, Danilo ; Yates, John R. ; Rodriguez, Henry. / Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles). In: Journal of Proteome Research. 2012 ; Vol. 11, No. 2. pp. 1412-1419.
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